name: DnaProteinAlignment version: 0.0.0.1 author: Christian Hoener zu Siederdissen, 2013 copyright: Christian Hoener zu Siederdissen, 2013 homepage: http://www.tbi.univie.ac.at/~choener/ maintainer: choener@tbi.univie.ac.at category: Bioinformatics license: GPL-3 license-file: LICENSE build-type: Simple stability: experimental cabal-version: >= 1.8.0 synopsis: Frameshift-aware alignment of protein sequences with DNA sequences description: Perform a semi-global alignment of a DNA sequence (local) with a protein sequence (global). The alignment includes the possibility of frame shifts. . The dynamic programming algorithm is created automatically from atomic single-tape grammars using our grammar product framework. . Run the program with @+RTS -N -RTS@ for optimal performance when aligning against a genome. . . . If you find this library or program useful, please cite: . @ Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler Product Grammars for Alignment and Folding submitted @ . @ Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler How to Multiply Dynamic Programming Algorithms Brazilian Symposium on Bioinformatics (BSB 2013) Lecture Notes in Bioinformatics 8213, Springer, Heidelberg @ Extra-Source-Files: BioInf/Alignment/DnaProtein.gra changelog library build-depends: ansi-wl-pprint , base >= 4 && < 5 , cmdargs == 0.10.* , ADPfusion >= 0.2.0.4 , array , BiobaseBlast >= 0.0.0.1 , BiobaseFasta >= 0.0.1.0 , BiobaseXNA >= 0.7.0.2 , biocore , bytestring , conduit , dlist , parallel , PrimitiveArray >= 0.5.1.0 , repa , split , vector exposed-modules: BioInf.Alignment.DnaProtein ghc-options: -O2 -fllvm -fsimpl-tick-factor=1000 executable DnaProteinAlignment build-depends: ansi-wl-pprint , base >= 4 && < 5 , cmdargs == 0.10.* , ADPfusion >= 0.2.0.4 , array , BiobaseBlast >= 0.0.0.1 , BiobaseFasta >= 0.0.1.0 , BiobaseXNA >= 0.7.0.2 , biocore , bytestring , conduit , dlist , DnaProteinAlignment , parallel , PrimitiveArray >= 0.5.1.0 , repa , split , vector ghc-options: -O2 -fllvm -fsimpl-tick-factor=1000 -threaded -rtsopts main-is: DnaProteinAlignment.hs source-repository head type: git location: git://github.com/choener/DnaProteinAlignment